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The flow channel design on bipolar plates affects proton exchange membrane (PEM) fuel cell performance by influencing reactant distribution and water removal in an operating fuel cell. The fuel cell performance can be improved by varying the type, size, or arrangement of channels. Two bio-inspired designs have been proposed by a research group at Oakland University, which results in improvement on the fuel cell performance. The objective of this research is to optimize the existing bio-inspired designs to further improve the fuel cell performance by the use of gates in the channel design to control the flow distribution. COMSOL Multiphysics software is used to model the flow field constrained by the Navier Stokes and Brinkman’s Equations. An interactive solver was developed between the COMSOL and MATLAB to find the optimal configuration of gate heights is required. An analytical model is also developed which will be used to verify the numerical results.